Phylogenetic profile of the response regulators and their binding site motifs. The RR gene trees on the left (top half, σ54-dependent RRs; bottom half, the other seven RRs), and the species tree at the top (based on 16S rRNA sequences) were created using FastTree on the MicrobesOnline platform . Numbers on the left indicate RRs by their DVU#. Species abbreviations used: M.xan, Myxococcus xanthus; An.K, Anaeromyxobacter sp. K; G.lov, Geobacter lovleyi; G.sul, Geobacter sulfurreducens; D.acet, Desulfotomaculum acetoxidans; Sy.th, Symbiobacterium thermophilum; T.ye, Thermodesulfovibrio yellowstonii; A.cap, Acidobacterium capsulatus; Tav, Thioalkalivibrio sp. HL-EGBR7; D.aro, Dechloromonas aromatica; D.auto, Desulfobacterium autotrophicum; D.alk, Desulfatibacillum alkenivornas; D.psy, Desulfotalea psychrophila; L.i, Lawsonia intracellularis; D.pig, Desulfovibrio piger; 27774, Desulfovibrio desulfuricans 27774; DvH, D. vulgaris Hildenborough; DvM, D. vulgaris Miyazaki; G20, Desulfovibrio desulfuricans G20; D.mag, Desulfovibrio magneticus; D.sal, Desulfovibrio salexigens; D.bac, Desulfomicrobium baculatum; D.ret, Desulfohalobium retbaense; S.fum, Syntrophobacter fumaroxidans. The two other sequenced D. vulgaris strains DP4 and RCH1 have an identical set of response regulators as the strain Hildenborough and are not shown in the figure. Orthologs were identified using the ortholog and tree browser functions on MicrobesOnline. Two RRs, DVU1083 and DVU3220, are conserved in all Desulfovibrio spp. Experimentally validated binding site motifs for the respective RRs are shown on the right. Motif logos were created using Weblogo  by using the sequences shown in Tables S7 (DAP-chip target based) and S9 (ortholog based) in Additional file 1. DAP, DNA affinity purified; RR, response regulator.